Perturbed Folding Kinetics of Circularly Permuted RNAs with Altered Topology

Heilman-Miller, Susan L.; Woodson, Sarah A.

doi:10.1016/s0022-2836(03)00304-8

Cited by 32 publications

(53 citation statements)

References 54 publications

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“…This permutation introduces a nick adjacent to a non-native base pairing, alt P3, that competes against P3 and causes the P3-P9 domain of the ribozyme to misfold (Pan and Woodson 1998). A nick in J8/7 is expected to disfavor alt P3 relative to P3, and may also facilitate conversion of misfolded intermediates to the native structure (Heilman-Miller and Woodson 2003). In agreement with these predictions, previous studies demonstrated that a significant portion of CP303 RNA refolds faster than L-21 ribozyme in splicing buffer (Heilman-Miller and Woodson 2003).…”

Section: Sequential Folding Of Cp303 Results In a Fast Folding Phasementioning

confidence: 99%

“…4). We previously characterized nine permuted RNAs, whose 5Ј and 3Ј ends are relocated to different regions of the ribozyme (Heilman-Miller and Woodson 2003). The transcripts are designated by the position of the 5Ј end.…”

Section: Effect Of Sequence Order On Sequential Rna Foldingmentioning

confidence: 99%

“…The CP RNAs form the correct tertiary structure and retain catalytic activity when refolded in splicing buffer. The refolding kinetics vary 10-fold among the permutants, however, demonstrating that the folding pathway is sensitive to the sequence distance between native interactions (Heilman-Miller and Woodson 2003). A CP RNA that begins near the natural 5Ј end refolds at nearly the same rate as the L-21 ribozyme, while RNAs that begin in the P4-P6 domain refold more slowly.…”

Section: Effect Of Sequence Order On Sequential Rna Foldingmentioning

confidence: 99%

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Effect of transcription on folding of the Tetrahymena ribozyme

Heilman-Miller

Woodson²

2003

RNA

101

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Sequential formation of RNA interactions during transcription can bias the folding pathway and ultimately determine the functional state of a transcript. The kinetics of cotranscriptional folding of the Tetrahymena L-21 ribozyme was compared with refolding of full-length transcripts under the same conditions. Sequential folding after transcription by phage T7 or Escherichia coli polymerase is only twice as fast as refolding, and the yield of native RNA is the same. By contrast, a greater fraction of circularly permuted variants folded correctly at early times during transcription than during refolding. Hybridization of complementary oligonucleotides suggests that cotranscriptional folding enables a permuted RNA beginning at G303 to escape nonnative interactions in P3 and P9. We propose that base pairing of upstream sequences during transcription elongation favors branched secondary structures that increase the probability of forming the native ribozyme structure.

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Section: Sequential Folding Of Cp303 Results In a Fast Folding Phasementioning

confidence: 99%

Section: Effect Of Sequence Order On Sequential Rna Foldingmentioning

confidence: 99%

Section: Effect Of Sequence Order On Sequential Rna Foldingmentioning

confidence: 99%

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Effect of transcription on folding of the Tetrahymena ribozyme

Heilman-Miller

Woodson²

2003

RNA

101

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“…[15][16][17][18][19] Interestingly, while folding of the Tetrahymena intron is affected by the different transcription rate of POLs from E. coli and T7-phage, 17 the RNAse P RNA (RNAP) did not respond to this difference in transcription speed. 20,21 The pioneering work of Sosnick, Pan and coworkers revealed that in addition to the elongation rate, transcriptional pausing, which is a property of bacterial POLs, and its duration affect RNA folding as well.…”

mentioning

confidence: 99%

RNA folding in living cells

Zemora

Waldsich

2010

RNA Biology

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“…19,20 Biophysical Methods to Study RNA Folding RNA folding occurs over a wide range of timescales and therefore also a wide range of methods have to be applied in order to study these processes ( Figure 5). For the initiation of the folding reaction mainly three methods are applied: changes in pH, 21 in temperature 22,23 or in ionic strength.…”

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confidence: 99%

Time‐resolved NMR studies of RNA folding

et al. 2007

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The application of real‐time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time‐resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long‐range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time‐resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non‐coding RNAs in cells. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 360–383, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Perturbed Folding Kinetics of Circularly Permuted RNAs with Altered Topology

Cited by 32 publications

References 54 publications

Effect of transcription on folding of the Tetrahymena ribozyme

Effect of transcription on folding of the Tetrahymena ribozyme

RNA folding in living cells

Time‐resolved NMR studies of RNA folding

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